Widespread occurrence and lateral transfer of the cyanobactin biosynthesis gene cluster in cyanobacteria

Abstract

Cyanobactins are small cyclic peptides produced by cyanobacteria. Here we demonstrate the widespread but sporadic occurrence of the cyanobactin biosynthetic pathway. We detected a cyanobactin biosynthetic gene in 48 of the 132 strains included in this study. Our results suggest that cyanobactin biosynthetic genes have a complex evolutionary history in cyanobacteria punctuated by a series of ancient horizontal gene transfer events.

FIG. 1.

Cyanobactin synthetase gene clusters in cyanobacteria. (a) The conserved cyanobactin protease genes, which can be detected using the primers designed in this work, are shaded. The peptide product of the gene cluster is presented in parentheses under the producer organism. (b) The primers cysF and cysR are aligned with cyanobactin synthetase gene sequences from seven cyanobacteria: Prochloron didemni (patA [AY986476]), Trichodesmium erythraeum IMS101 (triH [CP000393]), Lyngbya aestuarii CCY9616 (lynA [AAVU01000047]), Anabaena sp. 90 (unpublished), Nodularia spumigena CCY9414 (AAVW01000072.1), Microcystis aeruginosa NIES298 (mcaA [AM774406]), and Nostoc spongiaeforme subsp. tenue (tenA [EU290741]).

FIG. 2.

The sporadic distribution of cyanobactin synthetase genes in cyanobacteria. The phylogenetic tree is based on 71 16S rRNA gene sequences from strains analyzed in this study. The strains containing the cyanobactin synthetase genes are indicated on a gray background. The likelihood of each tree is expressed as the log likelihood (lnL). The maximum-likelihood tree (−lnL = 16083.13615) is based on 1,400 bp of the 16S rRNA gene sequence. Branch lengths are proportional to sequence change. Minimum-evolution and maximum-parsimony bootstrap values from 1,000 bootstrap replicates above 50 are given above and below the nodes. Outgroup taxa used to root the tree are not shown.

FIG. 3.

Phylogenetic incongruence between cyanobactin synthetase and 16S rRNA gene sequences. Maximum-likelihood trees are based on cyanobactin synthetase sequences and 16S rRNA gene sequences, respectively. The sequences used in the cyanobactin synthetase gene and 16S rRNA data sets were 1,300 bp and 1,400 bp, respectively. Branch lengths are proportional to sequence change. The substitution rates are in different scales in the trees. Minimum-evolution bootstrap values from 1,000 bootstrap replicates are at the nodes if the value is more than 70 and if the nodes were congruent with the nodes of the maximum-likelihood tree. Both of the trees are rooted at the midpoint.